LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# sample surface deposition script for molecules

units		lj
atom_style      bond
boundary        p p f

lattice		fcc 1.0
Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
region          box block 0 5 0 5 0 10
create_box      3 box bond/types 1 extra/bond/per/atom 1
Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874)
  1 by 1 by 1 MPI processor grid

region		substrate block INF INF INF INF INF 3
create_atoms	1 region substrate
Created 350 atoms
  Time spent = 0.000657082 secs

pair_style	lj/cut 2.5
pair_coeff	* * 1.0 1.0
pair_coeff	1 2 1.0 1.0 5.0
mass		* 1.0

bond_style	harmonic
bond_coeff      1 5.0 1.0

neigh_modify	delay 0

group		addatoms type 2
0 atoms in group addatoms
region          mobile block 0 5 0 5 2 INF
group		mobile region mobile
150 atoms in group mobile

compute		add addatoms temp
compute_modify	add dynamic/dof yes extra/dof 0

fix		1 addatoms nve
fix		2 mobile langevin 0.1 0.1 0.1 587283
fix		3 mobile nve

molecule        dimer molecule.dimer.shake
Read molecule dimer:
  2 atoms with max type 3
  1 bonds with max type 1
  0 angles with max type 0
  0 dihedrals with max type 0
  0 impropers with max type 0
region          slab block 0 5 0 5 8 9
fix		4 addatoms deposit 100 0 100 12345 region slab near 1.0                 mol dimer vz -1.0 -1.0 shake 6
fix		5 addatoms wall/reflect zhi EDGE
fix             6 all shake 0.0001 20 1000 b 1 mol dimer
  0 = # of size 2 clusters
  0 = # of size 3 clusters
  0 = # of size 4 clusters
  0 = # of frozen angles

thermo_style	custom step atoms temp epair etotal press
thermo          100
thermo_modify	temp add lost/bond ignore lost warn
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)

#dump		1 all atom 50 dump.deposit.atom

#dump		2 all image 50 image.*.jpg type type #		axes yes 0.8 0.02 view 80 -30
#dump_modify	2 pad 5

#dump		3 all movie 50 tmp.mpg type type #		axes yes 0.8 0.02 view 80 -30
#dump_modify	3 pad 5

run             10000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 5.3
  ghost atom cutoff = 5.3
  binsize = 2.65, bins = 3 3 6
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
SHAKE stats (type/ave/delta) on step 0
Per MPI rank memory allocation (min/avg/max) = 5.027 | 5.027 | 5.027 Mbytes
Step Atoms Temp E_pair TotEng Press 
       0      350            0   -6.9215833   -6.9215833   -1.0052629 
     100      352    1.0079368   -6.8875167   -6.8803581  -0.73353914 
     200      354    1.0079368   -6.8593854    -6.845149  -0.70414703 
     300      356    1.0098741   -6.8174079   -6.7961324    -0.691981 
     400      358     1.015821   -6.7853803   -6.7570054  -0.70383202 
     500      360    1.0431742   -6.7504367   -6.7142154  -0.68490175 
     600      362    1.0978772   -6.7139711   -6.6684789   -0.6851563 
     700      364    1.0536935   -6.6722083     -6.62155  -0.66701737 
     800      366    1.0615842   -6.6397391    -6.581729  -0.68874151 
     900      368    1.1690777   -6.6124387   -6.5409597   -0.6631748 
SHAKE stats (type/ave/delta) on step 1000
  1 1 2.33147e-15
    1000      370    1.2238341   -6.5840994    -6.501408  -0.68752603 
    1100      372    1.0648652    -6.557204   -6.4784841  -0.67502685 
    1200      374    1.1172515   -6.5811189   -6.4914998  -0.67901522 
    1300      376   0.90409242   -6.5843683    -6.506222  -0.63816276 
    1400      378    0.7557157   -6.5929671   -6.5229934  -0.58917374 
    1500      380   0.84878624   -6.5750822   -6.4913204  -0.68236463 
    1600      382    0.7649257   -6.5590761   -6.4789792  -0.66149637 
    1700      384    0.7158335   -6.5532553   -6.4740289  -0.59288863 
    1800      386   0.71794608   -6.5599255   -6.4762271  -0.61004271 
    1900      388   0.65121754   -6.5536032   -6.4738794  -0.64961438 
SHAKE stats (type/ave/delta) on step 2000
  1 1 2.9976e-15
    2000      390   0.69034633   -6.5451174   -6.4566114  -0.67204138 
    2100      392   0.64581391   -6.5535183   -6.4670253  -0.65563645 
    2200      394   0.65761022   -6.5431965   -6.4513982  -0.72677062 
    2300      396    0.6528782    -6.554984   -6.4601848  -0.64557524 
    2400      398   0.65836233   -6.5570075   -6.4577569  -0.69592521 
    2500      400    0.6411519   -6.5498234   -6.4496434  -0.72785753 
    2600      402   0.55292699   -6.5815848   -6.4921812  -0.64848109 
    2700      404   0.49353048   -6.5774182   -6.4949596  -0.72662195 
    2800      406   0.55912601   -6.5808134   -6.4844124  -0.75266257 
    2900      408   0.51233032    -6.571748   -6.4807089  -0.67844491 
SHAKE stats (type/ave/delta) on step 3000
  1 1 1.9984e-15
    3000      410   0.47624368   -6.5904636   -6.5033458  -0.72887592 
    3100      412   0.45076116   -6.5887249   -6.5039336  -0.67815331 
    3200      414   0.50910708   -6.5995831    -6.501205  -0.78059594 
    3300      416   0.45275554   -6.5991184   -6.5093291  -0.71529909 
    3400      418   0.38977308   -6.6018891    -6.522629  -0.69785747 
    3500      420   0.43625362   -6.6049671   -6.5140809  -0.69363556 
    3600      422   0.48184349    -6.613181   -6.5104182  -0.72994587 
    3700      424   0.39971995   -6.5997664   -6.5125634  -0.68093342 
    3800      426   0.43158248   -6.6067065   -6.5104616   -0.7865976 
    3900      428   0.39156456    -6.591465   -6.5022651  -0.72788973 
SHAKE stats (type/ave/delta) on step 4000
  1 1 1.66533e-15
    4000      430   0.45520202   -6.6043002   -6.4984393  -0.76339306 
    4100      432   0.37804217   -6.5825484   -6.4928509    -0.677846 
    4200      434   0.44408719   -6.6044968   -6.4970564  -0.72092913 
    4300      436   0.45187505   -6.6214439   -6.5100298  -0.71003531 
    4400      438   0.44634852   -6.6370982   -6.5250016   -0.7259646 
    4500      440   0.44774369   -6.6482048   -6.5337249  -0.75067855 
    4600      442   0.38004568   -6.6303883   -6.5315076  -0.70235189 
    4700      444   0.39828448   -6.6228295   -6.5174277  -0.78272067 
    4800      446   0.44085367   -6.6270343    -6.508419  -0.66562901 
    4900      448   0.47288585    -6.660755   -6.5314503  -0.74826687 
SHAKE stats (type/ave/delta) on step 5000
  1 1 1.77636e-15
    5000      450   0.43761136   -6.6799555   -6.5583968  -0.78360367 
    5100      452     0.411973    -6.678564   -6.5623548  -0.70194168 
    5200      454   0.40797743   -6.6866303   -6.5698086  -0.80152835 
    5300      456   0.34469092   -6.6716537   -6.5714968  -0.67613535 
    5400      458   0.34013914   -6.6730911   -6.5728318  -0.76078338 
    5500      460   0.34154783   -6.6605085   -6.5584154  -0.77667767 
    5600      462   0.36897691    -6.659394   -6.5475828  -0.81373456 
    5700      464    0.3540965   -6.6625103    -6.553763  -0.78251629 
    5800      466    0.4082091   -6.6773565   -6.5503387  -0.70767517 
    5900      468     0.447614   -6.7033749      -6.5623  -0.71623466 
SHAKE stats (type/ave/delta) on step 6000
  1 1 2.9976e-15
    6000      470   0.40113913    -6.679345   -6.5513219  -0.76250746 
    6100      472   0.42232629   -6.6963163   -6.5598656  -0.86594326 
    6200      474   0.39623605   -6.7100181   -6.5804473  -0.73732824 
    6300      476   0.37197778   -6.7159803   -6.5928994  -0.77305419 
    6400      478   0.33247467   -6.7128004   -6.6015118  -0.64546345 
    6500      480   0.34120281   -6.7088232   -6.5933119  -0.90961564 
    6600      482    0.3342529   -6.7056782   -6.5912555  -0.82385057 
    6700      484   0.34349872   -6.7152033   -6.5963272  -0.73664697 
    6800      486   0.33490767   -6.7243451   -6.6071963  -0.71978984 
    6900      488   0.36292075   -6.7126402   -6.5843536  -0.74097013 
SHAKE stats (type/ave/delta) on step 7000
  1 1 2.55351e-15
    7000      490   0.37409279   -6.7221689   -6.5885643  -0.71570235 
    7100      492    0.3742131   -6.7256916   -6.5906859  -0.70045361 
    7200      494   0.35928736   -6.7227141   -6.5917997  -0.83125489 
    7300      496   0.31306304   -6.7132829   -6.5980934  -0.80568965 
    7400      498     0.381634   -6.7248419   -6.5830702  -0.81697798 
    7500      500   0.36301318   -6.7268458   -6.5907159  -0.78210607 
    7600      502   0.34015711   -6.7204559   -6.5917112  -0.81197949 
    7700      504   0.33268221   -6.7140074   -6.5869413     -0.80133 
    7800      506   0.32240031   -6.7139558   -6.5897106  -0.78091826 
    7900      508   0.28597508   -6.7091152   -6.5979339  -0.80994821 
SHAKE stats (type/ave/delta) on step 8000
  1 1 2.44249e-15
    8000      510    0.3444676   -6.7275437   -6.5924583  -0.83444712 
    8100      512   0.34432983   -6.7402771    -6.604092  -0.79667718 
    8200      514   0.30652597   -6.7275717   -6.6053191  -0.79549578 
    8300      516   0.34347028   -6.7383117   -6.6001914  -0.81425668 
    8400      518   0.31465002   -6.7319759   -6.6044151  -0.77354562 
    8500      520   0.32120885   -6.7340886   -6.6028253  -0.83177871 
    8600      522   0.32040584     -6.71864   -6.5866721  -0.78525843 
    8700      524   0.34513435   -6.7414459   -6.5981888   -0.8520753 
    8800      526   0.32652464   -6.7316364   -6.5950672  -0.79191959 
    8900      528   0.29931888    -6.723678   -6.5975445  -0.86587625 
SHAKE stats (type/ave/delta) on step 9000
  1 1 2.10942e-15
    9000      530   0.34199152   -6.7390429   -6.5938579   -0.8478443 
    9100      532   0.32986081   -6.7434023   -6.6023434   -0.8020183 
    9200      534   0.32008917   -6.7313919   -6.5935258  -0.73850848 
    9300      536   0.31879033    -6.745493   -6.6072118  -0.88838081 
    9400      538   0.31905323   -6.7359144    -6.596551  -0.90024213 
    9500      540   0.30837753   -6.7292799   -6.5936509  -0.81564405 
    9600      542   0.34603468   -6.7371426    -6.583917  -0.78921543 
    9700      544   0.31957585   -6.7248739    -6.582416  -0.76240549 
    9800      546   0.32315085   -6.7357573   -6.5907537  -0.92679394 
    9900      548   0.34107078   -6.7519889   -6.5979469  -0.73569227 
SHAKE stats (type/ave/delta) on step 10000
  1 1 2.44249e-15
   10000      550   0.31059632   -6.7463923   -6.6052122  -0.75225652 
Loop time of 7.11276 on 1 procs for 10000 steps with 550 atoms

Performance: 607358.878 tau/day, 1405.923 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.9705     | 3.9705     | 3.9705     |   0.0 | 55.82
Bond    | 0.011102   | 0.011102   | 0.011102   |   0.0 |  0.16
Neigh   | 2.6732     | 2.6732     | 2.6732     |   0.0 | 37.58
Comm    | 0.20071    | 0.20071    | 0.20071    |   0.0 |  2.82
Output  | 0.0015368  | 0.0015368  | 0.0015368  |   0.0 |  0.02
Modify  | 0.21124    | 0.21124    | 0.21124    |   0.0 |  2.97
Other   |            | 0.0444     |            |       |  0.62

Nlocal:    550 ave 550 max 550 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    2331 ave 2331 max 2331 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    36458 ave 36458 max 36458 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 36458
Ave neighs/atom = 66.2873
Ave special neighs/atom = 0.363636
Neighbor list builds = 839
Dangerous builds = 0
Total wall time: 0:00:07
